BIOC 302 BIOCHEMISTRY II SPRING SEMESTER 2008

PREREQUISITES: BIOC 301, Biochemistry I

INSTRUCTOR: Dr. Jon Southard Office: Weyandt 239D

Phone: 357-2210 Email: southard@iup.edu

OFFICE HOURS: Monday – Friday, 12:00 noon to 1:00 pm (or other hours by appointment)

REQUIRED TEXT: Lehninger Principles of Biochemistry, Fourth Edition, D.L. Nelson and M.M. Cox,
Freeman and Company, Inc., New York, 2005

OPTIONAL SUPPLEMENT: The Absolute, Ultimate Guide to Lehninger Principles of Biochemistry Study
Guide and Solutions Manual, DM. Osgood and K Ocorr, Freeman and
Company, Inc., New York, 2005

COURSE WEBSITE: Accessible from: www.people.iup.edu/southard

The document “Learning Strategies for Biochemistry” provides suggestions for making
your study time productive as well as descriptions of the quizzes that will be given
during the course. Lecture PowerPoints will also be posted here. In addition, there
are links to a number of websites relevant to the course or to biochemistry in general.

COURSE DESCRIPTION AND OBJECTIVES

In this course we will employ our understanding of the structure and function of biomolecules to
investigate a number of biochemical processes. The unifying theme is the means by which organisms
orchestrate transformations of matter and energy in order to maintain the living state, in other words,
metabolism. Within this broad area, we will concentrate on pathways for energy production in animals
and pathways for harvesting light energy and synthesizing carbohydrates in photosynthetic organisms. We
will investigate other processes as time permits. It is not the objective of this course to survey all
important processes or to examine any process in exhaustive detail. The goal is to provide a number of
examples of how the fundamental concepts of biochemistry provide the framework to understand any
biological process at the most fundamental level.

GRADING: Grades will be determined by points earned on: a) exams; b) quizzes; c) class discussions of
problems or other contributions to class discussions; and d) oral reports on review articles relevant to
metabolism:
Regular exams (3 at 100 points each) 300
Comprehensive final exam 100
Quizzes (5 highest scores of six 10 pt quizzes) 50
Problem discussions/class contributions 50
Oral reports of review articles 50
Total 550

Course letter grades will be assigned based on the percentage of total points earned:
90-100% = A 80-89% = B 70-79% = C 60-69% = D <60% = F
EXAMS
The exams will be composed of short answer questions, essay-type questions, and problems generally
similar to the end-of-chapter problems. Exam items may be drawn from readings, lectures, or student
oral presentations of review articles. The tentative dates for the exams are given in the schedule at the
end of the syllabus.
The final exam will be comprehensive. A portion of the final will be based on topics covered since
the last regular exam. The rest of the exam will address important topics from any point in the course
and may require integration of material from throughout the course. The final exam is scheduled for
Wednesday, May 1, 8:00 am-10:00 am.
QUIZZES
There will be six quizzes during the semester. The quizzes are described under “Learning Strategies
for Biochemistry” on the course website. Each quiz will be announced (in class or by email) at least one
week in advance. The objective of the quizzes is to encourage you to complete important memorization
work as we begin the examination of various metabolic topics. Each quiz is worth a total of 10 points
(1/10 of an exam). The five highest quiz grades will be added to give the total points earned on quizzes.

PROBLEM DISCUSSIONS/CLASS CONTRIBUTIONS

Problems are found at the end of each chapter of the text. Additional problems may also be provided
by the instructor. It is recommended that students complete these problems as a check on
understanding of relevant facts, concepts, and skills. As time permits, class time will be designated for
discussion of these problems. Discussion periods will be announced in advance but students are advised
to spend time on these problems as they read the material (rather than wait for an announcement to
begin work on the problems). Student work on these problems will not be collected or graded. It is
expected that all students will make a conscientious effort to solve the problems. During discussion of
problems in class, students may be asked to present their work on particular problems.
The grade for this portion of the course will be assigned by the instructor based on the expectation
above as demonstrated by student contributions to discussions and presentations of their work (it is not
necessary to always 'get the right answer’). Group work on the assigned problems is encouraged.
Students may also earn points in this category by constructive contributions to the class. These may be
in the nature of asking relevant questions, answering questions posed by the instructor, or other actions
that positively affect the learning environment. Students may lose points in this category by repeated
actions that negatively affect the learning environment.

ORAL PRESENTATION OF A REVIEW ARTICLE

You will be assigned a review article by the instructor. All articles are obtainable free online via
PubMed (www.ncbi.nlm.nih.gov/gquery/gquery.fcgi) or journal websites. You should download the html
version of the article – this will allow you to incorporate figures from the article into your presentation.
You should prepare a 15 minute PowerPoint presentation based on the review. In your presentation,
you should:
a) Provide necessary background information to explain the significance of the area of research.
b) Explicitly connect the content of the review article to relevant course topics.
c) Describe how the review article goes beyond what we learned on those topics.
As the time for your presentation is limited, it may be appropriate to focus only on certain aspects of the
review (you do not need to address all the areas of the article). It is strongly advised that you
practice your presentation several times, beginning at least one week before your
presentation date. A copy of your PowerPoint file must be transmitted to the instructor by email on
the day of your presentation. Audience participation in these informal presentations is encouraged. Of
the 50 points for this portion of the course grade, 30 points will be based on the quality of your
presentation and 20 points will be based on your attendance at the presentations of other students.

GENERAL COURSE POLICIES

As a community of learners, participants in the course are expected to maintain an atmosphere of
civility in the classroom reflecting consideration and respect for others. There will be no eating or use
of tobacco products during class. A drink is permitted. Please turn off your cell phone/pager when you
enter the classroom. Punctuality is expected. If you are late, please do not disturb your classmates
when you enter.
Cooperative work is encouraged for all course activities excluding exam and quiz periods. It is
expected that an exam will be missed only because of a serious occurrence (serious illness, death in the
family, etc.). It is the responsibility of the student to inform the instructor of the reason for missing an
exam. This MUST be done in advance (in person, by phone message, or email) unless circumstances
CLEARLY do not allow advance notice. Written documentation must be presented to the instructor as
soon as possible.
 Attendance is required at all class meetings when student oral presentations are given. In addition,
points may be deducted for absence during class discussions of problems. Absences will be excused
only with written documentation of valid medical excuses or excuses for scheduled official University
activities or military duty.

TENTATIVE SCHEDULE FOR BIOC 302

Any changes will be announced as soon as possible. Changes in exam dates or topics will
be announced at least one week in advance of the actual exam date.

Class
Dates Topic/Activity Reading
meeting
syllabus, Text pp. 481-488
1 Jan 15 Intro to course & metabolism “Learning Strategies for
Biochemistry” (see course website)
2, 3 Jan 17, 22 Principles of bioenergetics Chapter 13
4, 5 Jan 24, 29 Glucose pathways Chapter 14
6, 7 Jan 31, Feb 5 Principles of metabolic regulation Chapter 15
8 Feb 7 catch-up/review
9 Feb 12 Exam #1: Chapters 13-15
10, 11 Feb 14, 19 Pryuvate dehyrogenase & citric acid cycle Chapter 16
12, 13 Feb 21, 26 Fatty acid catabolism Chapter 17
14, 15 Feb 28, Mar 4 Amino acid oxidation & urea cycle Chapter 18
16 Mar 6 Exam #2: Chapters 16-18
Spring Break
17, 18 Mar 18, 20 Oxidative phosphorylation Chapter 19 through 19.5
Photophosphorylation 19.6 to end of chapter 19
19 Mar 25
Carbohydrate synthesis in bacteria and plants Chapter 20 through 20.1
20 Mar 27 Lipid biosynthesis Chapter 21 (omit 21.2 & 21.3)
Chapter 22 (selected topics to be
21 Apr 1 Biosynthesis of amino acids and nucleotides
determined)
22 Apr 3 catch-up/review
23 Apr 8 Exam #3: Chapters 19-22
24 April 10 Integration & hormonal regulation of metabolism Chapter 23
25 April 15 Review article presentations 1-4
26 April 17 Review article presentations 5-8
27 April 22 Review article presentations 9-12
28 April 24 Review article presentations 13 & 14
29 May 1 Final exam (8:00 am – 10:00 am)